stuff

scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R

@@ -1,6 +1,6 @@
-#source("~/git/LSHTM_analysis/config/alr.R")
+source("~/git/LSHTM_analysis/config/alr.R")
-#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
-#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
 
 #=======
 # output
@@ -8,14 +8,31 @@
 #outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
 #cat("plots will output to:", outdir_images)
 
-custom_cor <- function(data, mapping, method, ...){
+custom_cor <- function(
+    data,
+    mapping,
+    method,
+    digits=2,
+    use="complete.obs",
+    stars=TRUE, 
+    ...
+){
   x <- eval_data_col(data, mapping$x)
   y <- eval_data_col(data, mapping$y)
   
-  corr <- cor(x, y, method=method, use='complete.obs')
+  corr_obj <- stats::cor.test(x, y, method=method, use=use)
+  cor_est <- as.numeric(corr_obj$estimate)
+  cor_txt <- formatC(cor_est, digits = digits, format = "f")
+  
+  cor_txt = paste0("ρ: ",as.character(round(cor_txt, 2)))
+  if (isTRUE(stars)) {
+    cor_txt <- str_c(cor_txt, signif_stars(corr_obj$p.value))
+  }
+  corr_obj$p.value
+  cor_txt
   
   ggally_text(
-    label = paste0("ρ: ",as.character(round(corr, 2))), 
+    label = cor_txt, 
     mapping = aes(),
     xP = 0.5, yP = 0.5,
     color = 'black',
@@ -24,22 +41,83 @@ custom_cor <- function(data, mapping, method, ...){
 }
 
 
+custom_corr2=function (data, mapping, ..., stars = TRUE, method = "pearson", 
+                       use = "complete.obs", display_grid = FALSE, digits = 3, 
+                       title_args = list(...), group_args = list(...), justify_labels = "right", 
+                       align_percent = 0.5, title = "ρ", alignPercent = warning("deprecated. Use `align_percent`"), 
+                       displayGrid = warning("deprecated. Use `display_grid`")) 
+{
+  if (!missing(alignPercent)) {
+    warning("`alignPercent` is deprecated. Please use `align_percent` if alignment still needs to be adjusted")
+    align_percent <- alignPercent
+  }
+  if (!missing(displayGrid)) {
+    warning("`displayGrid` is deprecated. Please use `display_grid`")
+    display_grid <- displayGrid
+  }
+  na.rm <- if (missing(use)) {
+    NA
+  }
+  else {
+    (use %in% c("complete.obs", "pairwise.complete.obs", 
+                "na.or.complete"))
+  }
   
-my_gg_pairs=function(plot_df, plot_title
+  
-                     , tt_args_size = 2.5
+  
-                     , gp_args_size = 2.5){
+  ggally_statistic(data = data,
+                   mapping = mapping,
+                   na.rm = na.rm, 
+                   align_percent = align_percent,
+                   display_grid = display_grid, 
+                   title_args = title_args, 
+                   group_args = group_args, 
+                   justify_labels = justify_labels, 
+                   justify_text = "left", 
+                   sep = if ("colour" %in% names(mapping)) 
+                     ": "
+                   else ": ", title = title, text_fn = function(x, y) {
+                     # if (is_date(x)) {
+                     #   x <- as.numeric(x)
+                     # }
+                     # if (is_date(y)) {
+                     #   y <- as.numeric(y)
+                     # }
+                     corObj <- stats::cor.test(x, y, method = method, 
+                                               use = use)
+                     cor_est <- as.numeric(corObj$estimate)
+                     cor_txt <- formatC(cor_est, digits = digits, format = "f")
+                     if (isTRUE(stars)) {
+                       cor_txt <- str_c(cor_txt, signif_stars(corObj$p.value))
+                     }
+                     cor_txt
+                   })
+}
+
+
+
+
+
+my_gg_pairs=function(
+    plot_df, 
+    plot_title
+    , tt_args_size = 5
+    , gp_args_size = 5
+){
   ggpairs(plot_df,
           columns = 1:(ncol(plot_df)-1),
           upper = list(
-            continuous = wrap(custom_cor, method="spearman"
+            continuous = wrap(
-              # ggally_cor, # ggally_cor()
+              #ustom_cor, method="spearman"
-              # method = "spearman",
+              custom_corr2, # ggally_cor()
-              # use = "pairwise.complete.obs",
+              method = "spearman",
-              # title="XXX ρ",
+              use = "pairwise.complete.obs",
-              # digits=2,
+              #title="XXX ",
-              # justify_labels = "centre",
+              digits=2,
-              # title_args=list(size=tt_args_size, colour="black")#,#2.5
+              justify_labels = "centre",
-              # #group_args=list(size=gp_args_size)#2.5
+              title_args=list(size=tt_args_size, colour="black")#,#2.5
+              #group_args=list(size=gp_args_size)#2.5
+              , size=10
             )
           ),
           lower = list(
@@ -80,7 +158,7 @@ corr_plotdf = corr_data_extract(merged_df3
 
 aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
 static_cols =  c("Log10(MAF)"
-                 #, "Log10(OR)"
+                 # , "Log10(OR)"
 )
 ############################################################
 #=============================================
@@ -175,6 +253,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
                                #, gp_args_size = 4
 )
 
+
 #### Combine plots #####
 # #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)
 # png(paste0(outdir_images